We evaluated the occurrence of Cryptosporidium and Giardia in the Lake Baroon catchment, Queensland, Australia. A total of 132 water samples were collected from 6 sites as well as from raw influent and treated effluent from a local sewage treatment plant (STP), over a 12-month period. Three new sites close to the entrance of the lake were added following initial assessment. The prevalence of faecal indicator organisms, E. coli and enterococci was also examined. There was no clear relationship between the level of indicator organisms, rainfall or the detection of Cryptosporidium and Giardia for most sites. Of the five sites showing levels of contamination with Cryptosporidium, only three coincided with elevated rainfall. The highest level of Cryptosporidium oocysts detected in the raw influent from the STP, coincided with the occurrence of an outbreak of cryptosporidiosis in the local area but no Cryptosporidium was detected in surface water samples during that period. Our results indicate that while the human contribution of Cryptosporidium is minimal, the high level of faecal indicator bacteria in surface water was not always associated with the presence Cryptosporidium in this catchment.